Closed Yyeserin closed 2 years ago
I think it is the problem with your parallel and treemix. provide a path as export PATH=$PATH:/home/directory/where/parallel/is and the same for the actual tree mix tool export PATH=$PATH:/home/directory/where/treemix/is. Then run step 1.
Hi again,
My problem seems to be solved now after calling parallel and treemix packages. Thank for the advice!
Hi!
I am trying to run the software in linux using the code below just for trial. I am sure that phylip exe works fine.
_sh ./Step1TreeMix.sh populations.treemix.gz 1 3 noRoot 3 /home/yeserin/snphylo/phylip-3.697/exe/consense 3spine 1 3 3
I keep getting the error pasted to the end.
I checked the line 49 in Step1_TreeMix.sh: __seq 1 $nboot | parallel -j$ncore dowork {} $infile $blockk $outname > $outname"_logfile_constree_bootrep.log"__
Is the problem related to the core usage, or something else?
I can provide more information if needed. I appreciate any help/suggestions a lot!
Best, Yeserin.
ERROR
_ Running TreeMix ./Step1_TreeMix.sh: line 49: parallel: command not found Running TreeMix: DONE gzip: bootstrap/3spine_constree_bootrep_1.treeout.gz: No such file or directory gzip: bootstrap/3spine_constree_bootrep_2.treeout.gz: No such file or directory gzip: bootstrap/3spine_constree_bootrep_3.treeout.gz: No such file or directory Bootstrap procedure: DONE Phylip - consensus tree construction: START Phylip - consensus tree construction: DONE Running TreeMix with consensus tree adding 1 to 3 migration edges ./Step1_TreeMix.sh: line 116: treemix: command not found ./Step1_TreeMix.sh: line 116: treemix: command not found ./Step1_TreeMix.sh: line 116: treemix: command not found ./Step1_TreeMix.sh: line 116: treemix: command not found ./Step1_TreeMix.sh: line 116: treemix: command not found ./Step1_TreeMix.sh: line 116: treemix: command not found ./Step1_TreeMix.sh: line 116: treemix: command not found ./Step1_TreeMix.sh: line 116: treemix: command not found ./Step1TreeMix.sh: line 116: treemix: command not found TreeMix - Bootstrap Analysis with migrations: DONE